PhD Chapter 1

Campaign 2016 - Maps and exploration


This series of files compile analyses done for the specific analysis of Chapter 1, for the regional campaign of 2016.

All analyses have been done with PRIMER-e 6 and R 4.1.0.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

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We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).

As data is missing for metal concentrations outside BSI, two Designs have been used:


1. Statistics

Calculation of basic statistics for each variable considered:

  Mean SD SE Median Min Max 95% CI
depth 20.235 16.929 2.582 17.600 1.000 65.900 5.060
om 0.856 0.891 0.136 0.491 0.209 3.863 0.266
gravel 0.043 0.092 0.014 0.000 0.000 0.359 0.028
sand 0.612 0.381 0.058 0.702 0.000 1.001 0.114
silt 0.285 0.328 0.050 0.116 0.000 0.942 0.098
clay 0.060 0.106 0.016 0.016 0.000 0.415 0.032
S 4.930 3.135 0.478 4.000 0.000 13.000 0.937
N 18.977 24.421 3.724 12.000 0.000 140.000 7.299
H 1.124 0.613 0.093 1.213 0.000 2.307 0.183
J 0.744 0.291 0.044 0.835 0.000 1.000 0.087
arsenic 4.300 4.759 0.971 2.500 0.800 21.300 1.904
cadmium 0.153 0.048 0.010 0.145 0.080 0.270 0.019
chromium 49.667 24.539 5.009 40.500 17.000 111.000 9.817
copper 9.787 7.764 1.585 7.800 2.400 28.800 3.106
iron 45356.633 17343.813 3540.291 39733.450 21938.100 85408.600 6938.843
manganese 776.662 362.884 74.073 677.850 318.400 1657.100 145.181
mercury 0.023 0.017 0.004 0.019 0.007 0.091 0.007
lead 5.421 3.021 0.617 4.650 1.900 12.200 1.209
zinc 59.358 30.340 6.193 47.700 26.900 141.400 12.138
  Mean SD SE Median Min Max 95% CI
depth 20.527 17.297 3.011 15.300 3.400 61.900 5.901
om 0.476 0.389 0.068 0.315 0.168 1.597 0.133
gravel 0.049 0.147 0.026 0.000 0.000 0.809 0.050
sand 0.832 0.270 0.047 0.960 0.000 1.000 0.092
silt 0.095 0.180 0.031 0.023 0.000 0.650 0.061
clay 0.024 0.086 0.015 0.005 0.000 0.497 0.029
S 4.333 2.558 0.445 4.000 1.000 9.000 0.873
N 19.970 27.779 4.836 12.000 2.000 142.000 9.478
H 0.975 0.589 0.102 0.974 0.000 1.985 0.201
J 0.690 0.302 0.053 0.840 0.000 1.000 0.103

2. Maps

2.1. General map

2.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Richness

Density

Diversity

Evenness

3. Figures

3.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions
Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes
Organic matter

Grain-size

Species abundances

Diversity indices

3.2. Phylum frequencies

Conditions
Phylum abundances by condition
Phylum HI R
Annelida 275 231
Echinodermata 230 162
Mollusca 196 189
Arthropoda 110 73
Platyhelminthes 3 0
Nematoda 1 0
Nemertea 1 0
Brachiopoda 0 2
Cnidaria 0 2

Regions
Phylum abundances by region
Phylum BSI CPC BDA MR
Annelida 206 69 188 43
Mollusca 151 45 89 100
Arthropoda 97 13 30 43
Echinodermata 24 206 24 138
Platyhelminthes 3 0 0 0
Nematoda 1 0 0 0
Nemertea 1 0 0 0
Brachiopoda 0 0 0 2
Cnidaria 0 0 0 2

3.3. Species estimation curves

3.4. Principal Component Analysis

Design 1

Variables have been standardized by mean and standard-deviation.

Design 2

Variables have been standardized by mean and standard-deviation.

3.5. Non-metric Multidimensional Scaling

Design 1

Variables have been standardized by mean and standard-deviation.

Design 2

Variables have been standardized by mean and standard-deviation.

Species

Stations with no species were deleted from this analysis.

3.6. Hierarchical Agglomerative Clustering

Design 1

Variables have been standardized by mean and standard-deviation.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65 
##   1   2   2   2   2   2   2   2   2   2   3   3   2   3   2   1   3   2   2   2   2   2 
##  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80  82  83  86  87  88  90  92 
##   2   2   2   2   2   1   1   1   1   2   1   2   2   2   3   3   3   2   2   2   3   1 
##  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 
##   3   2   1   3   1   3   1   1   3   2   3   3   1   2   1   3   2   1   3   1   2   2 
## 115 116 117 118 119 120 121 122 123 124 
##   2   3   3   3   2   2   1   2   3   3

Design 2

Variables have been standardized by mean and standard-deviation.

## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 
##   1   2   1   1   3   3   3   1   3   3   3   3   3   3   3   2   2   2   2   3   3   3 
## 123 124 
##   3   2

Species

Stations with no species were deleted from this analysis.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61  62  63  64  65 
##   1   1   1   1   1   1   1   1   1   2   1   1   3   1   2   2   1   2   2   2   1   1 
##  66  67  68  69  70  71  72  73  74  75  76  77  78  79  82  83  86  87  90  92  93  94 
##   1   1   3   1   2   2   1   1   2   2   1   1   2   2   1   3   1   2   1   2   3   3 
##  95  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
##   1   1   3   1   3   3   1   1   1   1   1   1   1   1   1   1   1   3   1   3   1   1 
## 117 118 119 120 121 122 123 124 
##   1   1   1   2   1   3   1   1


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